Ideos

query	Length
45S	9382
26S	1544
5.8S	157
18S	1552
5S	259
CS-237_satelite	557
CsatSD_centromere_237bp	237
CsatSD_subtelomere_370bp	370

Ideo function

source("Rfunctions.R")

t4 <- Sys.time()

sampd <- list.dirs("/media/knausb/E737-9B48/releases/scaffolded/")
sampd <- grep("scaffolded/$", sampd, value = TRUE, invert = TRUE)
sampd <- grep("EDTAOutput", sampd, value = TRUE, invert = TRUE)

#sampd <- sampd[ c(2:5, grep("EH23", sampd)) ]
#sampd <- sampd[ c(2:11, grep("EH23", sampd)) ]

#sampd <- sampd[ c(1:2, grep("EH23", sampd)) ]
#sampd <- sampd[ c(1:10, grep("EH23", sampd)) ]

#sampd <- sampd[ c(1:16, grep("EH23", sampd)) ]
#sampd <- sampd[ c(1:22, grep("EH23", sampd)) ]
#sampd <- sampd[ 1:30 ]
#sampd <- sampd[2:5]

#undebug(plot_ideo)
# p1 <- plot_ideo( sampd[1] )
# p1 <- plot_ideo( sampd[5] )
# p1 <- plot_ideo( sampd[6] )
# p1

# plist[[1]] <- plot_ideo( sampd[1] )
# plist[[2]] <- plot_ideo( sampd[2] )
# 
# plist[[1]]
# plist[[2]]


plist <- vector( mode = "list", length = length(sampd) )
for( i in 1:length(sampd) ){
  message("Processing sample ", i, " of ", length(sampd), ".")
  plist[[i]] <- plot_ideo( sampd[i] )
}

# plist[[1]]

#sub(".+//", "", sampd)
#sampn <- unlist(lapply(strsplit(sampd, split = "//"), function(x){x[2]}))

#, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome."}

library(ggpubr)

my_ps <- 1:4
#ggarrange( plotlist = plist[my_ps], ncol = 2, nrow = 3, labels = c("A", "B", "C", "D", "E", "F"))


for(i in 1:ceiling(length(plist)/4) ){
  my_ps <- 1:4
  my_ps <- my_ps + (i - 1) * 4
  if( my_ps[length(my_ps)] > length(plist) ){
    my_ps <- my_ps[1]:length(plist)
  }
  print(ggarrange( plotlist = plist[my_ps], ncol = 2, nrow = 2,
                   labels = c("A", "B", "C", "D")))
}

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green. The probe ‘CsatSD_centromere_237bp’ is in Dodger blue (#1E90FF), the probe ‘CsatSD_centromere_370bp’ is in magenta (#FF00FF)

# for(i in 1:(length(plist)/6) ){
#   my_ps <- 1:6
#   my_ps <- my_ps + (i - 1) * 6
#   if( my_ps[length(my_ps)] > length(plist) ){
#     my_ps <- my_ps[1]:length(plist)
#   }
#   print(ggarrange( plotlist = plist[my_ps], ncol = 2, nrow = 3, labels = c("A", "B", "C", "D", "E", "F")))
# }



#ggarrange( plotlist = plist[1:6], ncol = 2, nrow = 3, labels = c("A", "B", "C", "D", "E", "F"))
#ggarrange( plotlist = plist[7:12], ncol = 2, nrow = 3, labels = c("A", "B", "C", "D", "E", "F"))

t99 <- Sys.time()
t99 - t1

## Time difference of 4.820672 mins

Ideos

2023-02-26

Queries

nuccomp

fast_win

Ideo function